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31 January 2013

repmis: misc. tools for reproducible research in R

I've started to put together an R package called repmis. It has miscellaneous tools for reproducible research with R. The idea behind the package is to collate commands that simplify some of the common R code used within knitr-type reproducible research papers.

It's still very much in the early stages of development and has two commands:

LoadandCite: a command to load all of the R packages used in a paper and create a BibTeX file containing citation information for them. It can also install the packages if they are on CRAN.

source_GitHubData: a command for downloading plain-text formatted data stored on GitHub or at any other secure (https) URL.

I've written about why you might want to use source_GitHubData before (see here and here).

You can use LoadandCite in a code chunk near the beginning of a knitr reproducible research document to load all of the R packages you will use in the document and automatically generate a BibTeX file you can draw on to cite them. Here's an example:

LoadandCite draws on knitr's write_bib command to create the bibliographies, so each citation is given a BibTeX key like this: R-package_name. For example the key for the xtable package is R-xtable. Be careful to save the citations in a new .bib file, because LoadandCite overwrites existing files.

Citation of R packages is very inconsistent in academic publications. Hopefully by making it easier to cite packages more people will do so.

2 comments:

Have you considered a method to specify package versions in LoadandCite? Since packages change over time, it is useful to specify which versions were used. I proposed to deal with this problem with a works_with_R() header in The difficulty of reproducible research using R.